Ligand profile

CHEMBL409416

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00781 — Peptide deformylase

Via homolog UniProt Q9JN24 Formula C₃₂H₅₁N₅O₄
pchembl 8.52 ~3.0 nM
Mol. weight 569.79 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL409416
UniProt (similar protein)
Q9JN24
pchembl
8.520 (~3.0 nM)
Target protein
KP13_00781

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 569.79 Da
LogP (Crippen) 3.66
H-bond donors 2
H-bond acceptors 7
TPSA 96.43 Ų
Rotatable bonds 13
Aromatic rings 1 / 4
Heavy atoms 41
Fraction sp³ C 0.72
Formula C₃₂H₅₁N₅O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 96.4
  • −1 ≤ LogP ≤ 5 3.66
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 569.8
  • LogP ≤ 5 3.66
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 96.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)[C@H](NC(=O)[C@H](CC1CCCC1)CN(O)C=O)C(=O)c1ccc(N2CCN(CCN3CCCC3)CC2)cc1
InChI 
InChI=1S/C32H51N5O4/c1-32(2,3)30(33-31(40)27(23-37(41)24-38)22-25-8-4-5-9-25)29(39)26-10-12-28(13-11-26)36-20-18-35(19-21-36)17-16-34-14-6-7-15-34/h10-13,24-25,27,30,41H,4-9,14-23H2,1-3H3,(H,33,40)/t27-,30-/m1/s1
InChIKey 
GDWMRCWXJMKQFZ-POURPWNDSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF01327

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00781.

PDB 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 99

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)